Group 01 project: Analysis of Gene Expression in Parkinsson Disease
Introduction
Gene expression data (Affymetrix platform).
Collected from the blood of: - 20 healthy patients - 40 patients diagnosed with sporadic Parkinsons disease
Cleaning and Filtering Dataset
Arranging samples by condition
Filter out AFFX related spikes
Reshaping into tidy format
Statistical Analyses:
- Differential Expression of known biomarker gene
Results - Diff. Expression
Results - Diff. Expression of known biomarkers
Neurodegenerative-associated genes
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::: {style=“background-color: white; padding: 10px; display:”} ![ndg_boxplot]()
Results - Diff. Expression of known biomarkers
Pro-inflammatory genes
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::: {style=“background-color: white; padding: 10px; display:”} ![ndg_boxplot]()
Conclusion
- No clustering / Separtion along the PC’s
- No significant differentially expressed genes
- What to do next?
- With patient metadata, clustering might present itself
- Non-linear tendencies. Performing UMAP or t-SNE could provide clustering
- ANN, KNN logistic modelling could reveal expression patterns
- Redo the experiment
- Perhaps blood transcriptomics on PD patient, isn’t the way to go, though biomarker discovery would be ideal.